+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16505 | |||||||||
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Title | Cryo-EM captures early ribosome assembly in action | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome / ribosome assembly / ribosome biogenesis / total reconstitution / RNA / ribosomal protein. | |||||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / DNA-templated transcription termination / mRNA 5'-UTR binding / large ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
Authors | Lauer S / Nikolay R / Qin B | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM captures early ribosome assembly in action. Authors: Bo Qin / Simon M Lauer / Annika Balke / Carlos H Vieira-Vieira / Jörg Bürger / Thorsten Mielke / Matthias Selbach / Patrick Scheerer / Christian M T Spahn / Rainer Nikolay / Abstract: Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal ...Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. To obtain insights into the still unexplored early assembly phase of the bacterial 50S subunit, we exploited a minimal in vitro reconstitution system using purified ribosomal components and scalable reaction conditions. Time-limited assembly assays combined with cryo-EM analysis visualizes the structurally complex assembly pathway starting with a particle consisting of ordered density for only ~500 nucleotides of 23S rRNA domain I and three ribosomal proteins. In addition, our structural analysis reveals that early 50S assembly occurs in a domain-wise fashion, while late 50S assembly proceeds incrementally. Furthermore, we find that both ribosomal proteins and folded rRNA helices, occupying surface exposed regions on pre-50S particles, induce, or stabilize rRNA folds within adjacent regions, thereby creating cooperativity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16505.map.gz | 97.3 MB | EMDB map data format | |
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Header (meta data) | emd-16505-v30.xml emd-16505.xml | 30.2 KB 30.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16505_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_16505.png | 61.9 KB | ||
Masks | emd_16505_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-16505.cif.gz | 8.1 KB | ||
Others | emd_16505_half_map_1.map.gz emd_16505_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16505 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16505 | HTTPS FTP |
-Related structure data
Related structure data | 8c98MC 8c8xC 8c8yC 8c8zC 8c90C 8c91C 8c92C 8c93C 8c94C 8c95C 8c96C 8c97C 8c99C 8c9aC 8c9bC 8c9cC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16505.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.25 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16505_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16505_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16505_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : large ribosomal subunit precursor d12_L23
+Supramolecule #1: large ribosomal subunit precursor d12_L23
+Macromolecule #1: 50S ribosomal protein L34
+Macromolecule #2: 50S ribosomal protein L4
+Macromolecule #3: 50S ribosomal protein L13
+Macromolecule #4: 50S ribosomal protein L15
+Macromolecule #5: 50S ribosomal protein L20
+Macromolecule #6: 50S ribosomal protein L21
+Macromolecule #7: 50S ribosomal protein L22
+Macromolecule #8: 50S ribosomal protein L23
+Macromolecule #9: 50S ribosomal protein L24
+Macromolecule #10: 50S ribosomal protein L29
+Macromolecule #11: 50S ribosomal protein L30
+Macromolecule #12: 23S rRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 82.0 K / Max: 83.0 K |
Software | Name: Leginon |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 31000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Software | Name: Coot (ver. 0.9.6.2) |
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Refinement | Space: REAL |
Output model | PDB-8c98: |